Since the development of simple, aqueous protocols for the synthesis of anisotropic metal nanoparticles, research into many promising, valuable applications of gold nanorods has grown considerably, but a number of challenges remain, including gold particle yield, robustness to minor impurities, and precise control of gold nanorod surface chemistry. Herein we present the results of a composite fractional factorial series of experiments designed to screen seven additional potential avenues of control and to understand the seed-mediated silver-assisted synthesis of gold nanorods. These synthesis variables are the amount of sodium borohydride used and the rate of stirring when producing seed nanoparticles, the age of and the amount of seeds added, the reaction temperature, the amounts of silver nitrate and ascorbic acid added, and the age of the reduced growth solution before seed nanoparticles are added to initiate rod formation. This statistical experimental design and analysis method, besides determining which experimental variables are important and which are not when synthesizing gold nanorods (and quantifying their effects), gives further insight into the mechanism of growth by measuring the degree to which variables interact with each other by mapping out their mechanistic connections. This work demonstrates that when forming gold nanorods by the reduction of auric ions by ascorbic acid onto seed nanoparticles, ascorbic acid determines how much gold is reduced, and the amount of seeds determine how it is divided, yet both influence the intrinsic growth rates, in both width and length, of the forming nanorods. Furthermore, this work shows that the reduction of gold proceeds via direct reduction on the surface of seeds and not through a disproportionation reaction. Further control over the length of gold nanorods can be achieved by tuning the amount of silver nitrate or the reaction temperature. This work shows that silver does not directly influence rod length or width, and a new primary role for silver is proposed as a catalyst promoting the reduction of gold on the ends of forming nanorods. Furthermore, this silver catalyst is removed from the reaction by adsorption onto the surface of the growing nanorod. This work also demonstrates the importance of freshly prepared silver nitrate and ascorbic acid solutions, free from even a few hours of photodegradation, in preparing gold nanorods with high shape purity and gold yield.